So I beat the elite four and went to the spot on route 125 where kyogre is supposed to be. I'm pretty sure there is supposed to be a dark spot where you can dive down, but there isn't any for me. what should I do?
If the player does not reach Marine Cave fast enough, it will temporarily disappear and Terra Cave will appear. However, once Groudon is battled/caught in Terra Cave, or if the player did not arrive there fast enough, Marine Cave will reappear and relocate.
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